Water washing in over the transom and flooding the boat, and your air intake being a few inches closer to the water are two disadvantages that spring to mind.
Flooding is a particular problem going astern, my Destroyer used to fill up with any sort of speed astern and chopping a big lump out of the transom would have been the last thing I wanted to do on that, which was a fair bit bigger boat. You'd risk turning it into a submarine with a bit too much woof in reverse- and any sort of sea on the stern might be a bit wet on board too